Classical examination of tissue and cellular samples heavily relies on microscopy platforms, where molecular probes and a myriad of contrast agents are routinely used to investigate the molecular biology of cells. Nevertheless, a versatile, efficient and non-invasive approach to tag individual cells chosen upon observation is still lacking.
Here we describe cell labelling via photobleaching (CLaP), a method that enables instant, specific tagging of individual cells based on a phenotypic classification. This technique uses laser irradiation for crosslinking biotin on the plasma membrane of living cells and fluorescent streptavidin conjugates. Furthermore, the very same instrument used to image cells can tag them based on their morphological characteristics, dynamic behavior and localization within the sample at a given time, or any visible feature that distinguishes particular cells from the ensemble. The incorporated mark is stable, non-toxic, retained for several days, and transferred by cell division but not to adjacent cells in culture.
We combined CLaP with microfluidics-based single-cell capture followed by PCR assays and transcriptome-wide next-generation sequencing. We computed a number of quality control metrics to verify that CLaP does not interfere with protocols of sample preparation for transcriptomic experiments. To the best of our knowledge, CLaP is the first simple technology that allows correlating spatial and molecular information visible under a microscope when cells are individually sequenced.

Santiago Costantino

Associate professorUniversity of Montreal

Santiago Costantino received his PhD in ultrafast lasers from the Physics Department of the University of Buenos Aires in 2003. He moved to Canada for his postdoctoral training in microscopy and neuroscience at McGill University. He established his biophotonics lab at the Maisonneuve-Rosemont Hospital, Montreal University, in 2007. He is now an associate professor and his current research spans microengineering, image analysis and the development of medical tools for vision health.